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Appendix 3: Bibliography


Addison, R.F. and Clarke, K.R. (1990) ‘Biological effects of pollutants in a subtropical environment’, J. Exp. Mar. Biol. Ecol., 138.

Agard, J.B.R., Gobin, J. and Warwick, R.M. (1993) ‘Analysis of marine macrobenthic community structure in relation to pollution, natural oil seepage and seasonal disturbance in a tropical environment (Trinidad, West Indies)’, Mar. Ecol. Prog. Ser., 92, pp. 233–243.

Airoldi, L. (2000) ‘Responses of algae with different life histories to temporal and spatial variability of disturbance in subtidal reefs’, Mar. Ecol. Prog. Ser., 195, pp. 81–92.

Anderson, M.J. (2001a) ‘Permutation tests for univariate or multivariate analysis of variance and regression’, Can. J. Fish. Aquat. Sci., 58, pp. 626–639.

Anderson, M.J. (2001b) ‘A new method for non-parametric multivariate analysis of variance’, Austral Ecology, 26, pp. 32–46.

Anderson, M.J. (2006) ‘Distance-based tests for homogeneity of multivariate dispersions’, Biometrics, 62, pp. 245–253.

Anderson, M.J., Diebel, C.E., Blom, W.M. and Landers, T.J. (2005) ‘Consistency and variation in kelp holdfast assemblages: spatial patterns of biodiversity for the major phyla at different taxonomic resolutions’, J. Exp. Mar. Biol. Ecol., 320, pp. 35–56.

Anderson, M.J., Ford, R.B., Feary, D.A. and Honeywill, C. (2004) ‘Quantitative measures of sedimentation in an estuarine system and its relationship with intertidal soft-sediment infauna’, Mar. Ecol. Prog. Ser., 272, pp. 33–48.

Anderson, M.J., Gorley, R.N. and Clarke, K.R. (2008) PERMANOVA+ for PRIMER: Guide to software and statistical methods. Plymouth: PRIMER-E.

Anderson, M.J. and Underwood, A.J. (1997) ‘Effects of gastropod grazers on recruitment and succession of an estuarine assemblage: a multivariate and univariate approach’, Oecologia, 109, pp. 442–453.

Anderson, M.J. and Walsh, D.C.I. (2013) ‘PERMANOVA, ANOSIM and the Mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing?’, Ecol. Monog, 83, pp. 557–574.

Austen, M.C. and McEvoy, A.J. (1997) ‘The use of offshore meiobenthic communities in laboratory microcosm experiments: response to heavy metal contamination’, J. Exp. Mar. Biol. Ecol., 211, pp. 247–261.

Austen, M.C. and Somerfield, P.J. (1997) ‘A community level sediment bioassay applied to an estuarine heavy metal gradient’, Mar. Envir. Res., 43, pp. 315–328.

Austen, M.C. and Thrush, S.F. (2001) ‘Experimental evidence suggesting slow or weak response of nematode community structure to a large suspension-feeder’, J. Sea Res, 46, pp. 69–84.

Austen, M.C. and Warwick, R.M. (1989) ‘Comparison of univariate and multivariate aspects of estuarine meiobenthic community structure’, Est. Cstl. Shelf Sci, 29, pp. 23–42.

Austen, M.C. and Warwick, R.M. (1995) ‘Effects of manipulation of food supply on estuarine meiobenthos’, Hydrobiologia, 311, pp. 175–184.

Austen, M.C., Widdicombe, S. and Villano-Pitacco, N. (1998) ‘Effects of biological disturbance on diversity and structure of meiobenthic nematode communities’, Mar. Ecol. Prog. Ser., 174, pp. 233–246.

Bayne, B.L., Clarke, K.R. and Gray, J.S. (eds) (1988) ‘Biological effects of pollutants: results of a practical workshop’, Mar. Ecol. Prog. Ser., 46.

Bayne, B.L., Clarke, K.R. and Moore, M.N. (1981) ‘Some practical considerations in the measurement of pollution effects on bivalve molluscs, and some possible ecological consequences’, Aquatic toxicology , 1, pp. 159–174.

Belbin, L. (1991) ‘Semi-strong hybrid scaling, a new ordination algorithm’, J. Vegetat. Sci., 2, pp. 491–496.

Beukema, J.J. (1988) ‘An evaluation of the ABC–method (abundance /biomass comparison) as applied to macrozoobenthic communities living on tidal flats in the Dutch Wadden Sea’, Mar. Biol, 99, pp. 425–433.

Box, G.E.P. and Cox, D.R. (1964) ‘An analysis of transformations’, J. R. Statist. Soc. Ser. B, 26, pp. 211–243.

Bray, J.R. and Curtis, J.T. (1957) ‘An ordination of the upland forest communities of Southern Wisconsin’, Ecol. Monogr., 27, pp. 325–349.

Brown, B.E., Clarke, K.R. and Warwick, R.M. (2002) ‘Serial patterns of biodiversity change in corals across shallow reef flats in Ko Phuket, Thailand, due to the effects of local (sedimentation) and regional (climatic) perturbations’, Mar. Biol., 141, pp. 21–29.

Buchanan, J.B. (1993) ‘Evidence of benthic pelagic coupling at a station off the Northumberland coast’, J. Exp. Mar. Biol. Ecol., 172, pp. 1–10.

Caswell, H. (1976) ‘Community structure: a neutral model analysis’, Ecol. Monogr, 46, pp. 327–354.

Chapman, M.G. and Underwood, A.J. (1999) ‘Ecological patterns in multivariate assemblages: information and interpretation of negative values in ANOSIM tests’, Mar. Ecol. Prog. Ser., 180, pp. 257–265.

Chatfield, C. and Collins, A.J. (1980) Introduction to multivariate analysis. London: Chapman and Hall.

Clarke, K.R. (1988) ‘Detecting change in benthic community structure’, in Proceedings XIVth international biometric conference. Namur: Invited Papers. Societe Adolphe Quetelet, Gembloux, Belgium.

Clarke, K.R. (1990) ‘Comparisons of dominance curves’, J. Exp. Mar. Biol. Ecol., 138, pp. 143–157.

Clarke, K.R. (1993) ‘Non-parametric multivariate analyses of changes in community structure’, Aust. J. Ecol., 18, pp. 117–143.

Clarke, K.R. (1999) ‘Non-metric multivariate analysis in community-level ecotoxicology’, Environ. Toxicol. Chem., 18, pp. 118–127.

Clarke, K.R. and Ainsworth, M. (1993) ‘A method of linking multivariate community structure to environmental variables’, Mar. Ecol. Prog. Ser., 92, pp. 205–219.

Clarke, K.R., Chapman, M.G., Somerfield, P.J. and Needham, H.R. (2006) ‘Dispersion-based weighting of species counts in assemblage analyses’, Mar. Ecol. Prog. Ser, 320, pp. 11–27.

Clarke, K.R. and Gorley, R.N. (2006 or 2015) PRIMER v6 (or v7): User Manual/Tutorial. Plymouth: PRIMER-E.

Clarke, K.R. and Green, R.H. (1988) ‘Statistical design and analysis for a “biological effects” study’, Mar. Ecol. Prog. Ser, 46, pp. 213–226.

Clarke, K.R., Somerfield, P.J., Airoldi, L. and Warwick, R.M. (2006) ‘Exploring interactions by second-stage community analyses’, J. Exp. Mar. Biol. Ecol, 338, pp. 179–192.

Clarke, K.R., Somerfield, P.J. and Chapman, M.G. (2006) ‘On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages’, J. Exp. Mar. Biol. Ecol, 330, pp. 55–80.

Clarke, K.R., Somerfield, P.J. and Gorley, R.N. (2008) ‘Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage’, J. Exp. Mar. Biol. Ecol, 366, pp. 56–69.

Clarke, K.R., Tweedley, J.R. and Valesini, F.J. (2014) ‘Simple shade plots aid better long-term choices of data pre-treatment in multivariate assemblage studies’, J. Mar. Biol. Ass. UK, 94, pp. 1–16.

Clarke, K.R. and Warwick, R.M. (1994) ‘Similarity-based testing for community pattern: the 2-way layout with no replication’, Mar. Biol, 118, pp. 167–176.

Clarke, K.R. and Warwick, R.M. (1998a) ‘Quantifying structural redundancy in ecological communities’, Oecologia, 113, pp. 278–289.

Clarke, K.R. and Warwick, R.M. (1998b) ‘A taxonomic distinctness index and its statistical properties’, J. Appl. Ecol, 35, pp. 523–531.

Clarke, K.R. and Warwick, R.M. (1999) ‘The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels’, Mar. Ecol. Prog. Ser., 184, pp. 21–29.

Clarke, K.R. and Warwick, R.M. (2001) ‘A further biodiversity index applicable to species lists: variation in taxonomic distinctness’, Mar. Ecol. Prog. Ser., 216, pp. 265–278.

Clarke, K.R., Warwick, R.M. and Brown, B.E. (1993) ‘An index showing breakdown of seriation, related to disturbance, in a coral-reef assemblage’, Mar. Ecol. Prog. Ser., 102, pp. 153–160.

Clifford, D.H.T. and Stephenson, W. (1975) An introduction to numerical classification. New York: Academic Press.

Colebrook, J.M. (1986) ‘Environmental influences on long-term variability in marine plankton’, Hydrobiologia, 142, pp. 309–325.

Collins, N.R. and Williams, R. (1982) ‘Zooplankton communities in the Bristol Channel and Severn Estuary’, Mar. Ecol. Prog. Ser., 9, pp. 1–11.

Colwell, R.K. and Coddington, J.A. (1994) ‘Estimating terrestrial biodiversity through extrapolation’, Phil. Trans. Roy. Soc. B, 345, pp. 101–118.

Connell, J.H. (1974) ‘Field experiments in marine ecology’, in Mariscal, R. (ed.) Experimental marine biology. New York: Academic Press.

Connell, J.H. (1978) ‘Diversity in tropical rain forests and coral reefs’, Science N.Y, 199, pp. 1302–1310.

Cormack, R.M. (1971) ‘A review of classification’, J. R. Statist. Soc. Ser. A, 134, pp. 321–367.

Cox, T.F. and Cox, M.A.A. (2001) Multidimensional scaling. Chapman and Hall.

Danielidis, D.B. (1991) A systematic and ecological study of diatoms of the lagoons of Messolongi, Aitoliko and Kleissova (Greece). Ph.D. thesis,. University of Athens.

Dauvin, J.-C. (1984) Dynamique d’ecosystemes macrobenthiques des fonds sedimentaires de la Baie de Morlaix et leur perturbation par les hydrocarbures de l’Amoco-Cadiz. Doctoral thesis,. Univ. Pierre et Marie-Curie.

Dawson-Shepherd, A., Warwick, R.M., Clarke, K.R. and Brown, B.E. (1992) ‘An analysis of fish community responses to coral mining in the Maldives’, Environ. Biol. Fish, 33, pp. 367–380.

De’Ath, G. (2002) ‘Multivariate regression trees: a new technique for modeling species–environment relationships’, Ecology, 83(4), pp. 1105–1117.

Efron, B. (1979) ‘Bootstrap methods: Another look at the jack-knife’, Ann. Statist., 7, pp. 1–26.

Efron, B. and Tibshirani, R.J. (1993) An introduction to the bootstrap. Chapman and Hall.

Everitt, B. (1978) Graphical techniques for multivariate data. London: Heinemann.

Everitt, B. (1980) Cluster analysis. 2nd edn. London: Heinemann.

Faith, D.P. (1992) ‘Conservation evaluation and phylogenetic diversity’, Biol. Conserv., 61, pp. 1–10.

Faith, D.P. (1994) ‘Phylogenetic pattern and the quantification of organismal biodiversity’, Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 345, pp. 45–58.

Faith, D.P., Minchin, P.R. and Belbin, L. (1987) ‘Compositional dissimilarity as a robust measure of ecological distance’, Vegetatio, 69, pp. 57–68.

Field, J.G., Clarke, K.R. and Warwick, R.M. (1982) ‘A practical strategy for analysing multispecies distribution patterns’, Mar. Ecol. Prog. Ser., 8, pp. 37–52.

Fisher, R.A., Corbet, A.S. and Williams, C.B. (1943) ‘The relation between the number of species and the number of individuals in a random sample of an animal population’, J. anim. Ecol., 12, pp. 42–58.

Florek, K., Lukaszewicz, J., Perkal, J., Steinhaus, H. and Zubrzycki, S. (1951) ‘Sur la liason et la division des points d’un ensemble fini’, Colloquium Math, 2, pp. 282–285.

Gage, J.D. (1972) ‘Community structure of the benthos in Scottish sea-lochs. I. Introduction and species diversity’, Mar. Biol., 14, pp. 281–297.

Gage, J.D. and Coghill, G.G. (1977) ‘Studies on the dispersion patterns of Scottish sea-loch benthos from contiguous core transects’, in Coull, B. (ed.) Ecology of marine benthos. Columbia: University of South Carolina Press.

Gee, J.M. and Somerfield, P.J. (1997) ‘Do mangrove diversity and leaf litter decay promote meiofaunal diversity?’, J. Exp. Mar. Ecol. Biol., 218, pp. 13–33.

Gee, J.M. and Warwick, R.M. (1994a) ‘Metazoan community structure in relation to the fractal dimensions of marine microalgae’, Mar. Ecol. Prog. Ser., 103, pp. 141–150.

Gee, J.M. and Warwick, R.M. (1994b) ‘Body-size distribution in a marine metazoan community and the fractal dimensions of macroalgae’, J. Exp. Mar. Ecol. Biol., 178, pp. 247–259.

Gee, J.M., Warwick, R., Schaanning, M., Berge, J.A. and Ambrose Jr, W.G. (1985) ‘Effects of organic enrichment on meiofaunal abundance and community structure in sublittoral soft sediments’, J. Exp. Mar. Biol. Ecol., 91, pp. 247–262.

Goldman, N. and Lambshead, P.J.D. (1989) ‘Optimization of the Ewens/Caswell neutral model program for community diversity analysis’, Mar. Ecol. Prog. Ser., 50, pp. 255–261.

Gower, J.C. (1966) ‘Some distance properties of latent root and vector methods used in multivariate analysis’, Biometrika, 53, pp. 325–328.

Gower, J.C. (1971) ‘Statistical methods of comparing different multivariate analyses of the same data’, in Hodson, F.R., Kendall, D.G., and Tautu, P. (eds) Mathematics in the archaeological and historical sciences. Edinburgh: Edinburgh University Press, pp. 138–149.

Gower, J.C. and Ross, G.J.S. (1969) ‘Minimum spanning trees and single linkage cluster analysis’, Appl. Statist., 18, pp. 54–64.

Gray, J.S., Aschan, M., Carr, M.R., Clarke, K.R., Green, R.H., Pearson, T.H., Rosenberg, R. and Warwick, R.M.(1988) ‘Analysis of community attributes of the benthic macrofauna of Frierfjord/Langesundfjord and in a mesocosm experiment’, Mar. Ecol. Prog. Ser., 46, pp. 151–165.

Gray, J.S., Clarke, K.R., Warwick, R.M. and Hobbs, G. (1990) ‘Detection of initial effects of pollution on marine benthos: an example from the Ekofisk and Eldfisk oilfields, North Sea’, Mar. Ecol. Prog. Ser., 66, pp. 285–299.

Gray, J.S. and Pearson, T.H. (1982) ‘Objective selection of sensitive species indicative of pollution-induced change in benthic communities. I. Comparative methodology'. Mar. Ecol. Prog. Ser., 9, pp. 111–119.

Green, R.H. (1979) Sampling design and statistical methods for environmental biologists. New York: Wiley.

Greenacre, M.J. (1984) Theory and applications of correspondence analysis. London: Academic Press.

Hall, S.J. and Greenstreet, S.P. (1998) ‘Taxonomic distinctness and diversity measures: responses in marine fish communities’, Mar. Ecol. Prog. Ser., 166, pp. 227–229.

Hallett, C.S., Valesini, F.J. and Clarke, K.R. (2012) ‘A method for selecting health index metrics in the absence of independent measures of ecological condition’, Ecol. Indicat., 19, pp. 240–252.

Harper, J.L. and Hawksworth, D.L. (1994) ‘Biodiversity: measurement and estimation (preface)’, Phil. Trans. Roy. Soc. Lond. Ser. B, 345, pp. 5–12.

Heip, C., Herman, P.M.J. and Soetaert, K. (1988) ‘Data processing, evaluation, and analysis’, in Higgins, R.P. and Thiel, H. (eds) Introduction to the study of meiofauna. Washington DC: Smithsonian Institution, pp. 197–231.

Hill, M.O. (1973a) ‘Reciprocal averaging: an eigenvector method of ordination’, J. Ecol, 61, pp. 237–249.

Hill, M.O. (1973b) ‘Diversity and evenness: a unifying notation and its consequences’, Ecology, 54, pp. 427–432.

Hill, M.O. (1979a) DECORANA – A FORTRAN program for detrended correspondence analysis and reciprocal averaging. Ithaca, New York: Cornell University.

Hill, M.O. (1979b) TWINSPAN – A FORTRAN program for arranging multivariate data in an ordered two-way table by classification of individuals and attributes. Ithaca, New York: Cornell University.

Hill, M.O. and Gauch, H.G. (1980) ‘Detrended correspondence analysis, an improved ordination technique’, Vegetatio, 42, pp. 47–48.

Hope, A.C.A. (1968) ‘A simplified Monte Carlo significance test procedure’, J. R. Statist. Soc. Ser. B, 30, pp. 582–598.

Hourston, M., Platell, M.E., Valesini, F.J. and Potter, I.C. (2004) ‘Factors influencing the diets of four morphologically divergent fish species in nearshore marine waters’, J. Mar. Biol. Assoc. UK, 84, pp. 805–817.

Howson, C.M. (ed.) (1987) Directory of the British marine fauna and flora. Ross-on-Wye, Hertfordshire: Marine Conservation Society.

Humphries, C.J., Williams, P.H. and Vane-Wright, R.I. (1995) ‘Measuring biodiversity value for conservation’, Ann. Rev. Ecol. Syst., 26, pp. 93–111.

Hurlbert, S.H. (1971) ‘The nonconcept of species diversity: a critique and alternative parameters’, Ecology, 52, pp. 577–586.

Hurlbert, S.H. (1984) ‘Pseudoreplication and the design of ecological field experiments’, Ecol. Monogr., 54, pp. 187–211.

Huston, M. (1979) ‘A general hypothesis of species diversity’, Am. Nat., 113, pp. 81–101.

Ibanez, F. and Dauvin, J.-C. (1988) ‘Long-term changes (1977–1987) in a muddy fine sand Abra alba – Melinna palmata community from the Western English Channel: multivariate time-series analysis’, Mar. Ecol. Prog. Ser., 49, pp. 65–81.

Izsak, C. and Price, A.R.G. (2001) ‘Measuring β-diversity using a taxonomic similarity index, and its relation to spatial scale’, Mar. Ecol. Prog. Ser., 215, pp. 69–77.

Jayasree, K. (1976) Systematics and ecology of free-living marine nematodes from polluted intertidal sand in Scotland. Ph.D. thesis,. University of Aberdeen.

Jongman, R.H.G., ter Braak, C.F.J. and Tongeren, O.F.R. (1987) Data analysis in community and landscape ecology. Wageningen: Pudoc.

Kendall, M.A. and Widdicombe, S. (1999) ‘Small scale patterns in the structure of macrofaunal assemblages of shallow soft sediments’, J. Exp. Mar. Biol. Ecol., 237, pp. 127–140.

Kendall, M.G. (1970) Rank correlation methods. London: Griffin.

Kenkel, N.C. and Orloci, L. (1986) ‘Applying metric and nonmetric multidimensional scaling to some ecological studies: some new results’, Ecology, 67, pp. 919–928.

Kruskal, J.B. (1964) ‘Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis’, Psychometrika, 29, pp. 1–27.

Kruskal, J.B. and Wish, M. (1978) Multidimensional scaling. Beverley Hills, California: Sage Publications.

Krzanowski, W.J. (2002) ‘Multifactorial analysis of distance in studies of ecological community structure’, J. Agric. Biol. Environ. Stat., 7, pp. 222–232.

Kulczynski, S. (1928) ‘Die Pflanzenassoziationen der Pieninen’, Bull. Int. Acad. Pol. Sci. Lett. Cl. Sci. Math. Nat. Ser. B, Suppl II, pp. 57–203.

Lambshead, P.J.D. (1986) ‘Sub-catastrophic sewage and industrial waste contamination as revealed by marine nematode faunal analysis’, Mar. Ecol. Prog. Ser., 29, pp. 247–260.

Lambshead, P.J.D., Platt, H.M. and Shaw, K.M. (1983) ‘The detection of differences among assemblages of marine benthic species based on an assessment of dominance and diversity’, J. Nat. Hist., 17, pp. 859–874.

Lance, G.N. and Williams, W.T. (1967) ‘A general theory of classificatory sorting strategies: 1 Hierarchical Systems’, Comp. J., 9, pp. 373–380.

Legendre, P. and Anderson, M.J. (1999) ‘Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments’, Ecol. Monogr., 69, pp. 1–24.

Legendre, P. and Legendre, L. (2012) Numerical Ecology, 3rd English edition. Amsterdam: Elsevier.

Lek, E., Fairclough, D.V., Platell, M.E., Clarke, K.R., Tweedley, J.R. and Potter, I.C. (2011) ‘To what extent are the dietary compositions of three abundant, co-occurring labrid species different and related to latitude, habitat, body size and season?’, J. Fish Biol., 78, pp. 1913–1943.

Lorenzen, S. (1994) The phylogenetic systematics of free-living nematodes. London: Ray Society.

Magurran, A.E. (1991) Ecological diversity and its measurement. London: Chapman and Hall.

Mantel, N. (1967) ‘The detection of disease clustering and a generalized regression approach’, Cancer Res., 27, pp. 209–220.

Mardia, K.V., Kent, J.T. and Bibby, J.M. (1979) Multivariate analysis. London: Academic Press.

May, R.M. (1990) ‘Taxonomy as destiny’, Nature, 347, pp. 129–130.

McArdle, B.H. and Anderson, M.J. (2001) ‘Fitting multivariate models to community data: a comment on distance-based redundancy analysis’, Ecology, 82, pp. 290–297.

McEachran, J.D. and Miyake, T. (1990) ‘Phylogenetic interrelationships of skates: a working hypothesis (Chondrichthyes, Rajoidea). In: Elasmobranchs as living resources: advances in the biology, ecology, systematics, and the status of the fisheries’, in Pratt, H.L. et al. (eds.) NOAA technical report NMFS, pp. 285–304.

Morrisey, D.J., Underwood, A.J. and Howitt, L. (1996) ‘Effects of copper on the faunas of marine soft-sediments: an experimental field study’, Mar. Biol., 125, pp. 199–213.

Mumby, P.J., Clarke, K.R., and Harborne, A.R. (1996) ‘Weighting species abundance estimates for marine resource assessment’, Aquat. Conserv.: Mar. Freshw. Ecosyst., 6(3), pp. 115–120.

Nei, M. (1996) ‘Phylogenetic analysis in molecular evolutionary genetics’, Ann. Rev. Genet., 30, pp. 371–403.

Nelson, J.S. (1994) Fishes of the world, 3rd edn. New York: Wiley.

Ochiai, A. (1957) ‘Zoogeographic studies on the soleoid fishes found in Japan and its neighbouring regions’, Bull. Jpn. Soc. Sci. Fish, 22, pp. 526–530.

Olafsson, E. and Moore, C.G. (1992) ‘Effects of macroepifauna on developing nematode and harpacticoid assemblages in a subtidal muddy habitat’, Mar. Ecol. Prog. Ser., 84, pp. 161–171.

Olsgard, F. and Gray, J.S. (1995) ‘A comprehensive analysis of the effects of offshore oil and gas exploration and production on the benthic communities of the Norwegian continental shelf’, Mar. Ecol. Prog. Ser., 122, pp. 277–306.

Olsgard, F. and Somerfield, P.J. (2000) ‘Surrogates in marine benthic investigations – which taxonomic unit to target?’, J. Aquat. Ecosyst. Stress Recov., 7, pp. 25–42.

Olsgard, F., Somerfield, P.J. and Carr, M.R. (1997) ‘Relationships between taxonomic resolution and data transformations in analyses of a macrobenthic community along an established pollution gradient’, Mar. Ecol. Prog. Ser., 149, pp. 173–181.

Olsgard, F., Somerfield, P.J. and Carr, M.R. (1998) ‘Relationships between taxonomic resolution, macrobenthic community patterns and disturbance’, Mar. Ecol. Prog. Ser., 172, pp. 25–36.

Paul, W.L. and Anderson, M.J. (2013) ‘Causal modelling with multi-variate species data’, J. Exp. Mar. Biol. Ecol., 448, pp. 72–84.

Pearson, T.H. (1975) ‘The benthic ecology of Loch Linnhe and Loch Eil, a sea-loch system on the west coast of Scotland. IV. Changes in the benthic fauna attributable to organic enrichment’, J. Exp. Mar. Biol. Ecol., 20, pp. 1–41.

Pearson, T.H. and Blackstock, J. (1984) ‘Garroch Head sludge dumping ground survey’, final report, Dunstaffnage Marine Research Laboratory (unpublished}.

Pearson, T.H., Gray, J.S. and Johannessen, P.J. (1983) ‘Objective selection of sensitive species indicative of pollution-induced change in benthic communities. 2. Data analyses. Mar. Ecol. Prog. Ser., 12, pp. 237–255.

Pielou, E.C. (1975) Ecological diversity. New York: Wiley.

Pielou, E.C. (1984) The interpretation of ecological data. A primer on classification and ordination. New York: Wiley.

Piepenburg, D., Voss, J. and Gutt, J. (1997) ‘Assemblages of sea stars (Echinodermata: Asteroidea) and brittle stars (Echinodermata: Ophiuroidea) in the Weddell Sea (Antarctica) and off Northeast Greenland (Arctic): a comparison of diversity and abundance’, Polar Biology, 17, pp. 305–322.

Platell, M.E., Potter, I.C. and Clarke, K.R. (1998) ‘Resource partitioning by four species of elasmobranchs (Batoidea: Urolophidae) in coastal waters of temperate Australia’, Mar. Biol., 131, pp. 719–734.

Platt, H.M. and Warwick, R.M. (1983) Freeliving marine nematodes. Part I. British enoplids. Synopses of the british fauna no 28. Cambridge: Cambridge University Press.

Platt, H.M. and Warwick, R.M. (1988) Freeliving marine nematodes. Part II. British chromadorids. Leiden: E.J. Brill.

Potter, I.C., Bird, D.J., Claridge, P.N., Clarke, K.R., Hyndes, G.A. and Newton, L.C. (2001) ‘Fish fauna of the Severn Estuary. Are there long-term changes in abundance and species composition and are the recruitment patterns of the main marine species correlated?’, Mar. Ecol. Prog. Ser., 258, pp. 15–37.

Potter, I.C., Claridge, P.N., Hyndes, G.A. and Clarke, K.R. (1997) ‘Seasonal, annual and regional variations in ichthyofaunal compos¬ition in the inner Severn Estuary and inner Bristol Channel’, J. Mar. Biol. Assoc. U.K., 77, pp. 507–525.

Price, A.R.G., Keeling, M.J. and O’Callaghan, C.J. (1999) ‘Ocean-scale patterns of “biodiversity” of Atlantic asteroids determined from taxonomic distinctness and other measures’, Biol. J. Linn. Soc., 66, pp. 187–203.

Purcell, S.W., Rushworth, K., Clarke, K.R. and Dalton, S.J. (2014) ‘Defining critical habitats of threatened and endemic reef fishes using a multivariate approach’, Conserv. Biol. [Preprint].

Raffaelli, D. and Mason, C.F. (1981) ‘Pollution monitoring with meiofauna using the ratio of nematodes to copepods’, Mar. Poll. Bull., 12, pp. 158–163.

Reid, P.C., Barges, M.D.F. and Svendsen, E. (2001) ‘A regime shift in the North Sea circa 1988 linked to changes in the North Sea horse mackerel fishery’, Fish. Res., 50, pp. 163–171.

Rogers, S.I., Clarke, K.R. and Reynolds, J.D. (1999) ‘The taxonomic distinctness of coastal bottom-dwelling fish communities of the North-east Atlantic’, J. Anim. Ecol., 68, pp. 769–782.

Sanders, H.L. (1968) ‘Marine benthic diversity: a comparative study’, Am. Nat., 102, pp. 243–282.

Schafer, L.N., Platell, M.E., Valesini, F.J. and Potter, I.C. (2002) ‘Comparisons between the influence of habitat type, season and body size on the dietary compositions of fish species in nearshore marine waters’, J. Exp. Mar. Biol. Ecol., 278, pp. 67–92.

Scheffe, H. (1959) The analysis of variance. New York: Wiley.

Schiffman, S.S., Reynolds, M.L. and Young, F.W. (1981) Introduction to multi-dimensional scaling. Theory, methods and applications. London: Academic Press.

Schratzberger, M. and Warwick, R.M. (1998a) ‘Effects of physical disturbance on nematode communities in sand and mud: a microcosm experiment’, Mar. Biol., 130, pp. 643–650.

Schratzberger, M. and Warwick, R.M. (1998b) ‘Effects of the intensity and frequency of organic enrichment on two estuarine nematode communities’, Mar. Ecol. Prog. Ser., 164, pp. 83–94.

Schratzberger, M. and Warwick, R.M. (1999) ‘Differential effects of various types of disturbances on the structure of nematode assemblages: an experimental approach’, Mar. Ecol. Prog. Ser., 181, pp. 227–236.

Schwinghamer, P. (1981) ‘Characteristic size distributions of integral benthic communities’, Can. J. Fish. Aquat. Sci., 38, pp. 1255–1263.

Seber, G.A.F. (1984) Multivariate observations. New York: Wiley.

Shepard, R.N. (1962) ‘The analysis of proximities: multidimensional scaling with an unknown distance function’, Psychometrika, 27, pp. 125–140.

Shimatani, K. (2001) ‘On the measurement of species diversity incorporating species differences’, Oikos, 93, pp. 135–147.

Simpson, E.H. (1949) ‘Measurement of diversity’, Nature, 163, p. 688.

Smith, W.H. and Rissler, L.J. (2010) ‘Quantifying disturbance in terrestrial communities: Abundance-Biomass Comparisons of herpetofauna closely track forest succession’, Restor. Ecol., 18, pp. 195–204.

Sneath, P.H.A. (1957) ‘The application of computers to taxonomy’, J. Gen. Microbiol., 17, pp. 201–226.

Sneath, P.H.A. and Sokal, R.R. (1973) Numerical taxonomy. San Francisco: Freeman.

Sokal, R.R. and Rohlf, F.J. (1981) Biometry. San Francisco: Freeman.

Somerfield, P.J., Atkins, M., Bolam, S.G., Clarke, K.R., Garnacho, E., Rees, H.L. and Warwick, R.M. (2006) ‘Relative impacts at sites of dredged-material relocation in the coastal environment: a phylum-level meta-analysis approach’, Marine Biology, 148, pp. 1231–1240.

Somerfield, P.J., Clarke, K.R., Warwick, R.M. and Dulvy, N.K. (2008) ‘Average functional distinctness as a measure of the composition of assemblages’, ICES J. Mar. Sci., 65, pp. 1462–1468.

Somerfield, P.J. and Clarke, K.R. (1995) ‘Taxonomic levels, in marine community studies, revisited’, Mar. Ecol. Prog. Ser., 127, pp. 113–119.

Somerfield, P.J. and Clarke, K.R. (1997) ‘A comparison of some methods commonly used for the collection of sublittoral sediments and their associated fauna’, Mar. Environ. Res., 43, pp. 143–156.

Somerfield, P.J. and Clarke, K.R. (2013) ‘Inverse analysis in non-parametric multivariate analyses: distinguishing groups of associated species which covary coherently across samples’, J. Exp. Mar. Biol. Ecol., 449, pp. 261–273.

Somerfield, P.J., Clarke, K.R. and Olsgard, F. (2002) ‘A comparison of the power of categorical and correlational tests applied to community ecology data from gradient studies’, J. Anim. Ecol., 71, pp. 581–593.

Somerfield, P.J. and Gage, J.D. (2000) ‘Community structure of the benthos in Scottish sea-lochs. IV. Multivariate spatial pattern’, Mar. Biol., 136, pp. 1133–1145.

Somerfield, P.J., Gee, J.M. and Warwick, R.M. (1994a) ‘Benthic community structure in relation to an instantaneous discharge of waste water from a tin mine’, Mar. Pollut. Bull., 28, pp. 363–369.

Somerfield, P.J., Gee, J.M. and Warwick, R.M. (1994b) ‘Soft sediment meiofaunal community structure in relation to a long-term heavy metal gradient in the Fal estuary system’, Mar. Ecol. Prog. Ser., 105, pp. 79–88.

Somerfield, P.J., Gee, J.M. and Widdicombe, S. (1993) The use of meiobenthos in marine pollution monitoring programmes. Plymouth: Plymouth Marine Laboratory Miscellaneous Publication LIB-33A,B.

Somerfield, P.J., Olsgard, F. and Carr, M.R. (1997) ‘A further examination of two new taxonomic distinctness measures’, Mar. Ecol. Prog. Ser., 154, pp. 303–306.

Somerfield, P.J., Rees, H.L. and Warwick, R.M. (1995) ‘Interrelationships in community structure between shallow-water marine meiofauna and macrofauna in relation to dredgings disposal’, Mar. Ecol. Prog. Ser., 127, pp. 103–112.

Stephenson, W., Williams, W.T. and Cook, S.D. (1972) ‘Computer analysis of Petersen’s original data on bottom communities’, Ecol. Monogr., 42, pp. 387–415.

Stoffels, R.J., Clarke, K.R., Rehwinkel, R.A. and McCarthy, B.J. (2014) ‘Response of a floodplain fish community to river-floodplain connectivity: natural versus managed reconnection’, Can. J. Fish. Aquat. Sci., 71, pp. 236–245.

ter Braak, C.F.J. (1986) ‘Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis’, Ecology, 67, pp. 1167–1179.

ter Braak, C.F.J. and Smilauer, P. (2002) ‘CANOCO reference manual and CanoDraw for Windows user’s guide: software for canonical community ordination (v4.5)’. Microcomputer Power, Itaca.

Tweedley, J.R., Hallett, C.S., Warwick, R.M., Clarke, K.R. and Potter, I.C. (2015) ‘The hypoxia that developed in a microtidal estuary following an extreme storm produced dramatic changes in the benthos’, Mar. Freshw. Res., 67, pp. 327-341.

Underwood, A.J. (1981) ‘Techniques of analysis of variance in experimental marine biology and ecology’, Oceanogr. Mar. Biol. Ann. Rev., 19, pp. 513–605.

Underwood, A.J. (1992) ‘Beyond BACI: the detection of environ-mental impact on populations in the real, but variable, world’, J. Exp. Mar. Biol. Ecol., 161, pp. 145–178.

Underwood, A.J. (1997) Experiments in ecology: their logical design and interpretation using analysis of variance. Cambridge: Cambridge University Press.

Underwood, A.J. and Chapman, M.G. (1998) ‘A method for analysing spatial scales of variation in composition of assemblages’, Oecologia, 117, pp. 570–578.

Underwood, A.J. and Peterson, C.H. (1988) ‘Towards an ecological framework for investigating pollution’, Mar. Ecol. Prog. Ser., 46, pp. 227–234.

Valesini, F.J., Clarke, K.R., Eliot, I. and Potter, I.C. (2003) ‘A user-friendly quantitative approach to classifying nearshore marine habitats along a heterogeneous coast’, Est. Coast. Shelf Sci., 57, pp. 163–177.

Valesini, F.J., Tweedley, J.R., Clarke, K.R. and Potter, I.C. (2014) ‘The importance of regional, system-wide and local spatial scales in structuring temperate estuarine fish communities’, Estuar. Coasts, 37, pp. 525–547.

Vane-Wright, R.I., Humphries, C.J. and Williams, P.H. (1991) ‘What to protect? Systematics and the agony of choice’, Biol. Conserv., 55, pp. 235–254.

Veale, L., Tweedley, J.R., Clarke, K.R., Hallett, C.S. and Potter, I.C. (2014) ‘Characteristics of the ichthyofauna of a temperate microtidal estuary with a reverse salinity gradient, including inter-decadal comparisons’, J. Fish Biol., 85, pp. 1320–1354.

Warton, D.I., Wright, S.T. and Wang, Y. (2012) ‘Distance-based multivariate analyses confound location and dispersion effects’, Methods Ecol. Evol., 3, pp. 89–101.

Warwick, R.M. (1971) ‘Nematode associations in the Exe estuary’, J. Mar. Biol. Assoc. U.K, 51, pp. 439–454.

Warwick, R.M. (1984) ‘Species size distributions in marine benthic communities’, Oecologia (Berlin), 61, pp. 32–41.

Warwick, R.M. (1986) ‘A new method for detecting pollution effects on marine macrobenthic communities’, Mar. Biol., 92, pp. 557–562.

Warwick, R.M. (1988a) ‘Effects on community structure of a pollutant gradient – summary’, Mar. Ecol. Prog. Ser., 46, pp. 207–211.

Warwick, R.M. (1988b) ‘The level of taxonomic discrimination required to detect pollution effects on marine benthic communities’, Mar. Pollut. Bull., 19, pp. 259–268.

Warwick, R.M. (1993) ‘Environmental impact studies on marine communities: pragmatical considerations’, Aust. J. Ecol., 18, pp. 63–80.

Warwick, R.M., Ashman, C.M., Brown, A.R., Clarke, K.R., Dowell, B., Hart, B., Lewis, R.E., Shillabeer, N., Somerfield, P.J. and Tapp, J.F. (2002) ‘Inter-annual changes in the biodiversity and community stucture of the macrobenthos in Tees Bay and the Tees estuary, UK, associated with local and regional environ-mental events’, Mar. Ecol. Prog. Ser., 234, pp. 1–13.

Warwick, R.M. and Buchanan, J.B. (1970) ‘The meiofauna off the coast of Northumberland. I: The structure of the nematode population’, J. Mar. Biol. Assoc. U.K., 50, pp. 129–146.

Warwick, R.M., Carr, M.R., Clarke, K.R., Gee, J.M. and Green, R.H.(1988) ‘A mesocosm experiment on the effects of hydrocarbon and copper pollution on a sublittoral soft-sediment meiobenthic community’, Mar. Ecol. Prog. Ser., 46, pp. 181–191.

Warwick, R.M. and Clarke, K.R. (1991) ‘A comparison of methods for analysing changes in benthic community structure’, J. Mar. Biol. Assoc. U.K, 71, pp. 225–244.

Warwick, R.M. and Clarke, K.R. (1993a) ‘Comparing the severity of disturbance: a meta-analysis of marine macrobenthic community data’, Mar. Ecol. Prog. Ser., 92, pp. 221–231.

Warwick, R.M. and Clarke, K.R. (1993b) ‘Increased variability as a symptom of stress in marine communities’, J. Exp. Mar. Biol. Ecol., 172, pp. 215–226.

Warwick, R.M. and Clarke, K.R. (1994) ‘Relearning the ABC: taxonomic changes and abundance/biomass relationships in disturbed benthic communities’, Mar. Biol., 118, pp. 739–744.

Warwick, R.M. and Clarke, K.R. (1995a) ‘Multivariate measures of community stress and their application to marine pollution studies in the East Asian region’, Phuket Mar. Biol. Cent. Res. Bull., 60, pp. 99–113.

Warwick, R.M. and Clarke, K.R. (1995b) ‘New “biodiversity” measures reveal a decrease in taxonomic distinctness with increasing stress’, Mar. Ecol. Prog. Ser., 129, pp. 301–305.

Warwick, R.M. and Clarke, K.R. (1998) ‘Taxonomic distinctness and environmental assessment’, J. Appl. Ecol., 35, pp. 532–543.

Warwick, R.M. and Clarke, K.R. (2001) ‘Practical measures of marine biodiversity based on relatedness of species’, Oceanogr. Mar. Biol. Ann. Rev., 39, pp. 207–231.

Warwick, R.M., Clarke, K.R. and Gee, J.M. (1990) ‘The effects of disturbance by soldier crabs, Mictyris platycheles H. Milne Edwards, on meiobenthic community structure’. J. Exp. Mar. Biol. Ecol., 135, pp. 19–33.

Warwick, R.M., Clarke, K.R., and Suharsono (1990) ‘A statistical analysis of coral community responses to the 1982–3 El Nino in the Thousand Islands, Indonesia’, Coral reefs, 8, pp. 171–179.

Warwick, R.M. and Coles, J.W. (1977) ‘The marine flora and fauna of the Isles of Scilly. Free-living Nematoda’, J. Nat. Hist., 11, pp. 393–407.

Warwick, R.M. and Light, J. (2002) ‘Death assemblages of molluscs on st martin’s flats, isles of scilly: a surrogate for regional biodiversity?, Biodivers. Conserv., 11, pp. 99–112.

Warwick, R.M., Pearson, T.H., and Ruswahyuni (1987) ‘Detection of pollution effects on marine macrobenthos: further evaluation of the species abundance/biomass method’, Mar. Biol., 95, pp. 193–200.

Warwick, R.M., Platt, H.M., Clarke, K.R., Agard, J. and Gobin, J. (1990) ‘Analysis of macrobenthic and meiobenthic community structure in relation to pollution and disturbance in Hamilton Harbour, Bermuda’, J. Exp. Mar. Biol. Ecol., 138, pp. 119–142.

Warwick, R.M., Platt, H.M. and Somerfield, P.J. (1998) Freeliving marine nematodes. Part III. British Monhysterida. Synopses of the British Fauna No 38. EJ Brill, Dr. W. Backhuys for the Linnean Society of London and the Estuarine and Brackish-water Sciences Associatio.

Warwick, R.M. and Somerfield, P.J. (2008) ‘All animals are equal but some animals are more equal than others’, J. Exp. Mar. Biol. Ecol., 366, pp. 184–186.

Whittaker, R.H. (1952) ‘A study of summer foliage insect communities in the Great Smoky Mountains’, Ecol. Monogr., 22, pp. 1–44.

Widdicombe, S. and Austen, M.C. (1998) ‘Experimental evidence for the role of Brissopsis lyrifera (Forbes, 1841) as a critical species in the maintenance of benthic diversity and the modification of sediment chemistry’, J. Exp. Mar. Biol. Ecol., 228, pp. 241–255.

Widdicombe, S. and Austen, M.C. (2001) ‘The interaction between physical disturbance and organic enrichment: an important element in structuring benthic communities’, Limnol. Oceanog., 46, pp. 1720–1733.

Wilkinson, D.M. (1999) ‘The disturbing history of intermediate disturbance’, Oikos, 84, pp. 145–147.

Wilkinson, L. and Friendly, M. (2008) ‘The history of the cluster heat map’, Amer. Statist., 63, pp. 179–184.

Williams, P.H., Humphries, C.J. and Vane-Wright, R.I. (1991) ‘Measuring biodiversity: taxonomic relatedness for conservation priorities’, Aust. Syst. Bot., 4, pp. 665–679.

Woodd-Walker, R.S., Ward, P. and Clarke, A. (2002) ‘Large-scale patterns in diversity and community structure of surface water copepods from the Atlantic Ocean’, Mar. Ecol. Prog. Ser., 236, pp. 189–203.